Organism : Clostridium acetobutylicum | Module List :
Uncharacterized protein, ortholog of Thermotoga maritima (4981823) (NCBI ptt file)
Functional Annotations (1)
Regulation information for CAC0487(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for CAC0487
Module neighborhood information for CAC0487
|Gene||Common Name||Description||Module membership|
|CAC0122||cheY||Chemotaxis respons regulator (cheY) (NCBI ptt file)||167, 247|
|CAC0132||CAC0132||Hypothetical protein (NCBI ptt file)||247, 270|
|CAC0134||CAC0134||Hypothetical protein, CF-19 family (NCBI ptt file)||62, 247|
|CAC0135||CAC0135||Hypothetical protein, CF-23 family (NCBI ptt file)||13, 247|
|CAC0201||CAC0201||Transcriptional regulators, AcrR family (NCBI ptt file)||157, 259|
|CAC0238||CAC0238||ABC transporter, permease component (NCBI ptt file)||259, 346|
|CAC0291||CAC0291||FUSION: methionine sintase I (cobalamin dependent) and 5,10 methylenetetrahydrofolate reductase (NCBI ptt file)||259, 287|
|CAC0360||CAC0360||Transcriptional regulator, LacI family (HTH lacI domain), B.subtilis degA ortholog (NCBI ptt file)||10, 259|
|CAC0389||CAC0389||Hypothetical protein (NCBI ptt file)||167, 259|
|CAC0419||CAC0419||Predicted membrane protein (NCBI ptt file)||247, 351|
|CAC0420||CAC0420||Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file)||185, 247|
|CAC0421||CAC0421||Uncharacterized membrane protein (NCBI ptt file)||72, 259|
|CAC0477||CAC0477||AP superfamily (NCBI ptt file)||247, 258|
|CAC0487||CAC0487||Uncharacterized protein, ortholog of Thermotoga maritima (4981823) (NCBI ptt file)||247, 259|
|CAC0626||trpS||Tryptophan-tRNA synthetase, trpS (NCBI ptt file)||247, 296|
|CAC1273||CAC1273||Uncharacterized protein, YQEN B.subtilis homolog (NCBI ptt file)||146, 259|
|CAC1340||araR||Transcriptional regulator of the LacI family (NCBI ptt file)||259, 261|
|CAC1490||CAC1490||Hypothetical protein (NCBI ptt file)||185, 259|
|CAC1495||CAC1495||Enzyme of dihydrofolate reductase family, ortholog YWFD B.subtilis (NCBI ptt file)||5, 247|
|CAC1581||CAC1581||Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file)||185, 259|
|CAC1582||CAC1582||Membrane associated histidine kinase-like ATPase (NCBI ptt file)||259, 287|
|CAC1619||CAC1619||Hypothetical protein (NCBI ptt file)||71, 259|
|CAC1677||CAC1677||Predicted permease (NCBI ptt file)||259, 359|
|CAC2242||CAC2242||Predicted transcriptional regulator, arsE family (NCBI ptt file)||214, 247|
|CAC2429||CAC2429||Predicted membrane protein (NCBI ptt file)||259, 261|
|CAC2710||etfB||Electron transfer flavoprotein beta-subunit (NCBI ptt file)||255, 259|
|CAC2778||CAC2778||Rubredoxin (NCBI ptt file)||31, 259|
|CAC2779||CAC2779||Hypothetical protein (NCBI ptt file)||20, 259|
|CAC2780||CAC2780||Spore coat protein, cotF related (NCBI ptt file)||20, 259|
|CAC2824||CAC2824||N-terminal HKD family nuclease fused to DNA/RNA helicases of superfamily II,conserved in Streptomyces (NCBI ptt file)||154, 247|
|CAC2902||CAC2902||Isopentenyl monophosphate kinase, IPK (NCBI ptt file)||66, 247|
|CAC2973||kdgA||2-keto-3-deoxy-6-phosphogluconate aldolase, eda/kdgA (NCBI ptt file)||108, 247|
|CAC2996||CAC2996||Superfamily II DNA/RNA helicase, SNF2 family (NCBI ptt file)||259, 287|
|CAC3232||CAC3232||Hypothetical protein (NCBI ptt file)||62, 247|
|CAC3236||CAC3236||Possible transcriptional regulator from YAEG/LRPR family (NCBI ptt file)||247, 312|
|CAC3380||CAC3380||Metallo-beta-lactamase superfamily hydrolase (NCBI ptt file)||108, 247|
|CAC3481||CAC3481||Transcriptional regulator, AcrR family (NCBI ptt file)||167, 247|
|CAC3524||CAC3524||Hypothetical protein, CF-7 family (NCBI ptt file)||226, 247|
|CAC3529||CAC3529||Hypothetical protein (NCBI ptt file)||71, 259|
|CAC3530||CAC3530||Hypothetical protein (NCBI ptt file)||71, 259|
|CAC3531||CAC3531||IS605/IS200-like transposase (NCBI ptt file)||190, 247|
|CAC3546||CAC3546||Highly conserved protein containing a domain related to cellulase catalitic domain and a thioredoxin domain (NCBI ptt file)||259, 300|
|CAC3562||CAC3562||HD superfamily hydrolase (NCBI ptt file)||127, 247|
|CAC3563||CAC3563||Mismatch repair protein MutS-like ATPase (NCBI ptt file)||247, 335|
|CAC3591||CAC3591||Acyl-ACP thioesterase (NCBI ptt file)||157, 259|
|CAC3601||CAC3601||Nudix (MutT) family hydrolase (NCBI ptt file)||62, 259|
|CAC3649||spoVT||Possible stage V sporulation protein T, transcriptional regulator AbrB homolog (NCBI ptt file)||108, 247|
|CAC3677||kdpE||KDP operon transcriptional regulatory protein KdpE (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)||108, 247|
|CAC3687||CAC3687||Transcriptional regulator, AcrR family (NCBI ptt file)||140, 259|
Gene Page Help
If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.
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If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.
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Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.
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Module Members Tab
Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.
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CircVisOur circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
- 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
- 2. Source gene
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